Merge remote-tracking branch 'origin/pr/936'

Author: chrisgorgo

nipype/interfaces/camino/connectivity.py

@@ -12,22 +12,18 @@
 import os
 
 class ConmatInputSpec(CommandLineInputSpec):
-    in_file = File(exists=True, argstr='-inputfile %s',
-                   mandatory=True, position=1,
+    in_file = File(exists=True, argstr='-inputfile %s', mandatory=True,
                    desc='Streamlines as generated by the Track interface')
 
-    target_file = File(exists=True, argstr='-targetfile %s',
-                       mandatory=True, position=2,
+    target_file = File(exists=True, argstr='-targetfile %s', mandatory=True,
                        desc='An image containing targets, as used in ProcStreamlines interface.')
 
     scalar_file = File(exists=True, argstr='-scalarfile %s',
-                       position=3,
                        desc=('Optional scalar file for computing tract-based statistics. '
                              'Must be in the same space as the target file.'),
                        requires=['tract_stat'])
 
     targetname_file = File(exists=True, argstr='-targetnamefile %s',
-                           position=4,
                            desc=('Optional names of targets. This file should contain one entry per line, '
                                  'with the target intensity followed by the name, separated by white space. '
                                  'For example: '
@@ -39,7 +35,12 @@ class ConmatInputSpec(CommandLineInputSpec):
 
     tract_stat = traits.Enum("mean", "min", "max", "sum", "median", "var", argstr='-tractstat %s', units='NA',
                              desc=("Tract statistic to use. See TractStats for other options."),
-                             requires=['scalar_file'])
+                             requires=['scalar_file'],xor=['tract_prop'])
+
+    tract_prop = traits.Enum("length", "endpointsep", argstr='-tractstat %s', 
+                             units='NA', xor=['tract_stat'],
+                             desc=('Tract property average to compute in the connectivity matrix. '
+                                   'See TractStats for details.'))
 
     output_root = File(argstr='-outputroot %s', genfile=True,
         desc=('filename root prepended onto the names of the output files. '

nipype/interfaces/camino/tests/test_auto_Conmat.py

@@ -13,28 +13,29 @@ def test_Conmat_inputs():
     ),
     in_file=dict(argstr='-inputfile %s',
     mandatory=True,
-    position=1,
     ),
     output_root=dict(argstr='-outputroot %s',
     genfile=True,
     ),
     scalar_file=dict(argstr='-scalarfile %s',
-    position=3,
     requires=['tract_stat'],
     ),
     target_file=dict(argstr='-targetfile %s',
     mandatory=True,
-    position=2,
     ),
     targetname_file=dict(argstr='-targetnamefile %s',
-    position=4,
     ),
     terminal_output=dict(mandatory=True,
     nohash=True,
     ),
+    tract_prop=dict(argstr='-tractstat %s',
+    units='NA',
+    xor=['tract_stat'],
+    ),
     tract_stat=dict(argstr='-tractstat %s',
     requires=['scalar_file'],
     units='NA',
+    xor=['tract_prop'],
     ),
     )
     inputs = Conmat.input_spec()